Error in FUN(X[[i]], ...) : length(column) == nrow(table) is not TRUE

[MSajek]

Hi,
When I run the script make-data.R I have above mentioned error after 'Cleaning table cart '. I would be grateful for any help how to fix it.
Here is my sessionInfo:

R version 4.0.5 (2021-03-31)
Platform: x86_64-conda-linux-gnu (64-bit)
Running under: Ubuntu 20.04.3 LTS

Matrix products: default
BLAS/LAPACK: /home/marcin/anaconda3/envs/r4-base/lib/libopenblasp-r0.3.17.so

locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=pl_PL.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=pl_PL.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=pl_PL.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=pl_PL.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats graphics grDevices utils datasets methods base

other attached packages:
[1] magrittr_2.0.2 ENCODExplorer_2.16.0 stringi_1.7.5
[4] Ularcirc_1.8.0 data.table_1.14.2

loaded via a namespace (and not attached):
[1] MatrixGenerics_1.2.1 Biobase_2.50.0
[3] httr_1.4.2 tidyr_1.2.0
[5] bit64_4.0.5 jsonlite_1.8.0
[7] AnnotationHub_2.22.1 shiny_1.7.1
[9] assertthat_0.2.1 interactiveDisplayBase_1.28.0
[11] BiocManager_1.30.16 stats4_4.0.5
[13] BiocFileCache_1.14.0 blob_1.2.2
[15] BSgenome_1.58.0 GenomeInfoDbData_1.2.4
[17] Rsamtools_2.6.0 yaml_2.3.5
[19] BiocVersion_3.12.0 pillar_1.7.0
[21] RSQLite_2.2.10 lattice_0.20-45
[23] glue_1.6.2 digest_0.6.29
[25] GenomicRanges_1.42.0 promises_1.2.0.1
[27] XVector_0.30.0 htmltools_0.5.2
[29] httpuv_1.6.5 Matrix_1.4-0
[31] XML_3.99-0.9 pkgconfig_2.0.3
[33] zlibbioc_1.36.0 purrr_0.3.4
[35] xtable_1.8-4 later_1.3.0
[37] BiocParallel_1.24.1 tibble_3.1.6
[39] generics_0.1.2 IRanges_2.24.1
[41] ellipsis_0.3.2 cachem_1.0.6
[43] withr_2.5.0 SummarizedExperiment_1.20.0
[45] BiocGenerics_0.36.1 cli_3.2.0
[47] crayon_1.5.0 mime_0.12
[49] memoise_2.0.1 fansi_1.0.2
[51] tools_4.0.5 lifecycle_1.0.1
[53] matrixStats_0.61.0 stringr_1.4.0
[55] S4Vectors_0.28.1 DelayedArray_0.16.3
[57] AnnotationDbi_1.52.0 Biostrings_2.58.0
[59] compiler_4.0.5 GenomeInfoDb_1.26.7
[61] rlang_1.0.2 ENCODExplorerData_0.99.5
[63] grid_4.0.5 RCurl_1.98-1.6
[65] rstudioapi_0.13 rappdirs_0.3.3
[67] bitops_1.0-7 DBI_1.1.2
[69] curl_4.3.2 R6_2.5.1
[71] GenomicAlignments_1.26.0 dplyr_1.0.8
[73] rtracklayer_1.50.0 fastmap_1.1.0
[75] bit_4.0.4 utf8_1.2.2
[77] parallel_4.0.5 Rcpp_1.0.8.2
[79] vctrs_0.3.8 dbplyr_2.1.1
[81] tidyselect_1.1.2

[ericfournier2]

Hi,

ENCODE seems to have changed the format of certain tables, and others have grown so large that they cause timeouts when we parse them from an URL stream. I'm testing my fixes right now, and will get back to you once they're in.

Best regards,
-Eric